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Yorodumi- PDB-3ll1: Monomeric Griffithsin with a Single Gly-Ser Insertion and Mutatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ll1 | ||||||
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Title | Monomeric Griffithsin with a Single Gly-Ser Insertion and Mutations to Remove Residual Self-Association | ||||||
Components | Griffithsin | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / sugar-binding / anti-HIV / high mannose / Man9 / gp120 / gp41 / jacalin-related / Mannose-binding | ||||||
Function / homology | Function and homology information N-acetylgalactosamine binding / glucose binding / mannose binding / carbohydrate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Griffithsia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Moulaei, T. / Wlodawer, A. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Monomerization of viral entry inhibitor griffithsin elucidates the relationship between multivalent binding to carbohydrates and anti-HIV activity. Authors: Moulaei, T. / Shenoy, S.R. / Giomarelli, B. / Thomas, C. / McMahon, J.B. / Dauter, Z. / O'Keefe, B.R. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ll1.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ll1.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ll1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3ll1 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3ll1 | HTTPS FTP |
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-Related structure data
Related structure data | 3lkySC 3ll0C 3ll2C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12627.627 Da / Num. of mol.: 1 Mutation: Gly-Ser insertion after S16, L2S, E119D, Q120N, deltaY121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Griffithsia (eukaryote) / Strain: Q66D336 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84801 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 0.1M citric acid, 3M NaCl, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→50 Å / Num. obs: 65427 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.082 / Χ2: 1.45 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / Num. unique all: 6418 / Χ2: 0.935 / % possible all: 99.4 |
-Phasing
Phasing MR | Rfactor: 46.61 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LKY Resolution: 0.97→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.165 / WRfactor Rwork: 0.152 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.92 / SU B: 0.49 / SU ML: 0.014 / SU R Cruickshank DPI: 0.022 / SU Rfree: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.42 Å2 / Biso mean: 14.177 Å2 / Biso min: 7.51 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.97→0.995 Å / Total num. of bins used: 20
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